[b][u]UPDATE 10/19[/u]:[/b] As of Destiny 2 [url=https://www.bungie.net/en/Explore/Detail/Update/46410]Hotfix 1.0.5[/url], raid keys should no longer be erroneously removed when players create a new character, or when players log in to alternate characters for the first time after the weekly reset.
Additionally, raid keys are no longer removed at the weekly reset, in general.
[b]Prior Message[/b]
[spoiler]
Through our investigations with internal teams, we have identified two instances where Leviathan raid keys are erroneously removed from character inventory.
[quote][b]Signing in with alternate characters will remove raid keys if the character had not been signed in since the weekly reset.
If a player earns Raid keys and creates a new character, raid keys are removed from inventory.[/b][/quote]
To prevent this issue, we advise players sign in with all characters or inspect all characters on the Destiny Companion App prior to completing checkpoints within the Leviathan raid after the weekly reset.
Please note: Leviathan raid progress, including key rewards, are reset each week. We are looking to address issues where keys are removed erroneously with a future update. Stay tuned to @BungieHelp for future announcements. [/spoiler]

So I just completed the raid and had my three keys (Aqueduct, Pipeline, Irrigation). After completing we went to orbit and back in to go to the underbelly for the chests. Upon re-entering the raid my keys vanished. I was the only one in the fireteam this happened to. Any help would be fantastic.